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Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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qiuhai
April 01, 2019 04:45PM
Hi Peter,

Thank you for your response. Actually, your answer reminded me a warning information about deoblique at the beginning when I ran auto_warp.py. Then I took anther version of T1 image (skull stripped) from Freesurfer and the result of inverse warping looks reasonable now, although it is still a little off, but I think that might be due to the alignment between T1 and template.

I would still like to post the terminal output here, to see if you could help to check everything looks normal. Thanks! The AFNI version I used is AFNI_19.0.24 (Mar 8 2019)

Below are the terminal output for auto_warp.py

[Qiuhais-MacBook-Pro-2:~/jin/5006] qiuhai% auto_warp.py -base MNI_T1_ns.nii -input brain.nii -skull_strip_input no
#++ auto_warp.py version: 0.04
# Output directory /Users/qiuhai/jin/5006/awpy/
#Script is running:
mkdir /Users/qiuhai/jin/5006/awpy/
cd /Users/qiuhai/jin/5006/awpy/
#Script is running:
3dcopy /Users/qiuhai/jin/5006/brain.nii /Users/qiuhai/jin/5006/awpy/anat.nii
++ 3dcopy: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
#Script is running (command trimmed):
3dUnifize -GM -input ./anat.nii -prefix ./anat.un.nii
++ 3dUnifize: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
+ Pre-processing: ADV.....UWGm
++ Output dataset ./anat.un.nii
++ ===== CPU time = 51.8 sec Elapsed = 12.1
#Script is running:
3dcopy /Users/qiuhai/jin/5006/MNI_T1_ns.nii /Users/qiuhai/jin/5006/awpy/base.nii
++ 3dcopy: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
#++ Aligning /Users/qiuhai/jin/5006/awpy/base.nii data to /Users/qiuhai/jin/5006/awpy/anat.un.nii data
#Script is running (command trimmed):
@auto_tlrc -base ./base.nii -input ./anat.un.nii -suffix .aff -no_ss -no_pre -init_xform CENTER
Copying NIFTI volume to ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA
++ 3dcopy: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]

Performing center alignment with @Align_Centers

++ 3dcopy: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ 3drefit: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig
+ deoblique
++ 3drefit processed 1 datasets
++ 3drename: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ THD_rename_dataset_files: rename anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.HEAD -> __ats_tmp__anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.HEAD
++ THD_rename_dataset_files: rename anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.BRIK.gz -> __ats_tmp__anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.BRIK.gz
** THD_rename_dataset_files: old header anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+acpc.HEAD doesn't exist!
** THD_rename_dataset_files: old header anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+tlrc.HEAD doesn't exist!
++ 3dWarp: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
Center distance of 0.000015 mm
Padding ...
++ 3dZeropad: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ output dataset: ./__ats_tmp__ref_base.nii_40pad+tlrc.BRIK
Resampling ...
++ 3dcalc: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: A cast of thousands
++ 3dcalc: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: A cast of thousands
Clipping -0.000100 1566.890100 ...
++ 3dcalc: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: A cast of thousands
++ 3drefit: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___rs_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+tlrc.HEAD
+ changing dataset view code
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD
+ changing dataset view code
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD
+ changing dataset view code
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
Registration (linear final interpolation) ...
++ 3dWarpDrive: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
RMS[0] = 1884.17 851.388 ITER = 14/137
1884.17

Warping has converged.

++ 3dcopy: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ 3dWarp: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
Applying brain mask
++ 3dcalc: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: A cast of thousands
++ 3dWarp: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ 3drename: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ THD_rename_dataset_files: rename __ats_tmp___pad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+orig.HEAD -> __ats_tmp___pad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff.skl+orig.HEAD
++ THD_rename_dataset_files: rename __ats_tmp___pad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+orig.BRIK.gz -> __ats_tmp___pad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff.skl+orig.BRIK.gz
++ 3dcalc: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: A cast of thousands
Unpadding ...
++ 3dZeropad: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ output dataset: ./__ats_tmp___upad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+orig.BRIK
++ 3drefit: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+orig
*+ WARNING: Changing the space of an ORIG view dataset may cause confusion!
*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space).
*+ WARNING: Consider changing the view of the dataset to TLRC view also
++ 3drefit processed 1 datasets
Changing view of transformed anatomy
++ 3drefit: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+orig.HEAD
+ changing dataset view code
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
Setting parent with 3drefit -wset ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.HEAD __ats_tmp___upad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+tlrc
++ 3drefit: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA.aff+tlrc
+ setting Warp parent
++ 3drefit processed 1 datasets
++ 3dAFNItoNIFTI: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
Cleanup ...
++ 3drename: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Warning: ignoring +orig on new_prefix.
++ THD_rename_dataset_files: rename __ats_tmp___rs_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.HEAD -> __ats_tmp___rs_pre.anat.un+orig.HEAD
++ THD_rename_dataset_files: rename __ats_tmp___rs_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK.gz -> __ats_tmp___rs_pre.anat.un+orig.BRIK.gz
++ 3drename: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Warning: ignoring +orig on new_prefix.
++ THD_rename_dataset_files: rename pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.HEAD -> pre.anat.un+orig.HEAD
++ THD_rename_dataset_files: rename pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK.gz -> pre.anat.un+orig.BRIK.gz
#Script is running:
3dAttribute DELTA /Users/qiuhai/jin/5006/awpy/anat.un.aff.nii
#Script is running:
3dAttribute DELTA /Users/qiuhai/jin/5006/awpy/base.nii
2.000000 2.000000
#Script is running (command trimmed):
3dinfo -same_grid ./anat.un.aff.nii ./base.nii
#++ Aligning /Users/qiuhai/jin/5006/awpy/base.nii data to /Users/qiuhai/jin/5006/awpy/anat.un.aff.nii data
#Script is running (command trimmed):
3dQwarp -prefix ./anat.un.aff.qw.nii -blur -3 -3 -workhard:0:1 -base ./base.nii -source ./anat.un.aff.nii
++ OpenMP thread count = 12
++ 3dQwarp: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=1 xtop=2 ybot=2 ytop=5 zbot=5 ztop=0 voxels
++ Weightizing the base image
++ +++++++++++ Begin warp optimization: base=./base.nii source=./anat.un.aff.nii
++ AFNI warpomatic: 94 x 116 x 96 volume ; autobbox = 5..87 7..107 5..89 [clock= 502ms]
lev=0 0..93 0..115 0..95: [first cost=-0.81092] ..... done [cost:-0.81092==>-0.89414]
lev=1 patch=71x87x71 [clock= 11s 133ms]........:[cost=-0.94629]:........ done [cost:-0.89414==>-0.95986 ; 16 patches optimized, 0 skipped]
lev=2 patch=53x65x53 [clock= 16s 830ms]........................... done [cost:-0.95986==>-1.04325 ; 27 patches optimized, 0 skipped]
lev=3 patch=39x49x41 [clock= 22s 45ms]............... done [cost:-1.04325==>-1.11984 ; 50 patches optimized, 14 skipped]
lev=4 patch=29x37x31 [clock= 31s 648ms]................. done [cost:-1.11984==>-1.17822 ; 105 patches optimized, 45 skipped]
lev=5 patch=25x25x25 [clock= 40s 856ms]..................... done [cost:-1.17822==>-1.24541 ; 241 patches optimized, 151 skipped]
++ ========== total number of parameters 'optimized' = 5427
++ Output dataset ./anat.un.aff.qw.nii
++ Output dataset ./anat.un.aff.qw_WARP.nii
++ ===== CPU time = 333.8 sec clock time = 53s 854ms
#++ Applying warps to /Users/qiuhai/jin/5006/brain.nii
#Script is running (command trimmed):
3dNwarpApply -nwarp "./anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D" -master ./base.nii -source /Users/qiuhai/jin/5006/brain.nii -prefix ./brain.aw.nii
++ 3dNwarpApply: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is './base.nii'
++ opened source dataset '/Users/qiuhai/jin/5006/brain.nii'
++ Processing -nwarp
++ Warping:.Z
++ Output dataset ./brain.aw.nii
++ total CPU time = 3.3 sec Elapsed = 0.5
#++ Saving history
#Script is running (command trimmed):
3dNotes -h "auto_warp.py -base MNI_T1_ns.nii -input brain.nii \
-skull_strip_input no" ./brain.aw.nii


And below is the terminal output for 3dNwarpApply that I re-ran with -iwarp option:

[Qiuhais-MacBook-Pro-2:~/jin/5006] qiuhai% 3dNwarpApply -master brain.nii -dxyz 2 -source aal_MNI_V4.nii -iwarp -nwarp "awpy/anat.un.aff.qw_WARP.nii awpy/anat.un.aff.nii.Xaff12.1D" -ainterp NN -prefix aal_MNI_V4_NL_native.nii
++ 3dNwarpApply: AFNI version=AFNI_19.0.24 (Mar 8 2019) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is 'brain.nii'
++ output grid size = 2 mm
++ opened source dataset 'aal_MNI_V4.nii'
++ Processing -nwarp
+ -- invert max|AA|=40.394058
+ - init nstep=7 qq=1/2^7=0.007812
+ - start iterations: normAA=28.084309 inewtfac=0.273993
+ - iterate 1 nrat=0.029783
+ - iterate 2 nrat=0.021639
+ - iterate 3 nrat=0.019353
+ - iterate 4 nrat=0.012896
+ - iterate 5 nrat=0.010630
+ - iterate 6 nrat=0.006168
+ - iterate 7 nrat=0.004342
+ - iterate 8 nrat=0.002062
+ - iterate 9 nrat=0.001304
+ - iterate 10 nrat=0.000478
+ - switching from linear interp
+ - iterate 11 nrat=0.000187
+ - iterate 12 nrat=0.000063
+ -- iteration converged
++ Warping:.Z
++ Output dataset ./aal_MNI_V4_NL_native.nii
++ total CPU time = 61.4 sec Elapsed = 7.0
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Re: Nonlinear transform EPI data

qiuhai April 01, 2019 02:56PM

Re: Nonlinear transform EPI data

Peter Molfese April 01, 2019 03:51PM

Re: Nonlinear transform EPI data

qiuhai April 01, 2019 04:45PM

Re: Nonlinear transform EPI data Attachments

qiuhai April 02, 2019 01:12AM

Re: Nonlinear transform EPI data

qiuhai April 02, 2019 12:17PM

Re: Nonlinear transform EPI data

Peter Molfese April 02, 2019 12:25PM

Re: Nonlinear transform EPI data

qiuhai April 02, 2019 03:33PM

Re: Nonlinear transform EPI data

Peter Molfese April 03, 2019 10:23AM